This study aimed to discover whether using maltogenic amylase (MAse) to modify starch in germinated brown rice flour may enhance slow digestion starch and release more bioactive compounds (BCs) content. To achieve this aim, the starch was modified with four levels of MAse (0 U, 133 U, 266 U and 399 U MAse/g flour) for 1 hr at pH 5 and then spray-dried to make modified flour. The biochemical impacts of the products were then accessed in normal and type 2 diabetic mice for 4 weeks. The result showed that when the starch was modified by MAse 266 U/g, a significant reduction of rapidly digested starch to 22.35% from 61.56%, an increase in slowly digested starch to 33.09% while resistant starch as 2.92% corresponding to the increase of γ-amino butyric acid to 528.1 ± 44.1 mg/L and 120.6 ± 10.9 mg/L of ferulic acid. The extract from modified flour showed very strong cytotoxic activity against HepG2 cell (>80% inhibition). The result in vivo showed that the type-2 diabetic mice fed with this modified product could better improve the stability of the glycemic index. Also, atherosclerotic plaque assessment further supports these findings. The results indicated that BCs released considerably couple with the changes in starch properties caused by MAse enhanced the effectiveness of this product to diabetes as well as positive effect on cytotoxic activity against HepG2 cell.